Research workbench
Crystal structure of PI3K delta in complex with a 7-(3-(piperazin-1- YL)PHENYL)PYRROLO[2,1-F][1,2,4] triazin-4-amine deriviatine
Analyse Crystal structure of PI3K delta in complex with a 7-(3-(piperazin-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UBT
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform…
- EC
- 2.7.1.153
- UniProt
- O00329, P27986
- Ligands
- 85S
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) | protein | 911 | 44% helix, 18% strand | O00329 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 163 | 91% helix, 0% strand | P27986 |
Ligands and binding sites
- 85S · 1-[4-(3-{4-amino-5-[1-(oxan-4-yl)-1H-pyrazol-5-yl]pyrrolo[2,1-f][1,2,4]triazin-7-yl}phenyl)piperazin-1-yl]ethan-1-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.82 | 0.84 | 114 | empty |
| 2 | 930 | 0.81 | 0.83 | 89 | empty |
| 3 | 111 | 0.69 | 0.91 | 32 | empty |
| 4 | 303 | 0.69 | 0.84 | 44 | empty |
| 5 | 302 | 0.68 | 0.83 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 2210 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5UBT · Crystal structure of PI3K delta in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- O00329 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O00329
- Every structure of UniProt P27986
- Elsewhere: RCSB PDB 5UBT · PDBe 5UBT · UniProt O00329 · UniProt P27986
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